Dr. Roy Thinks about Ethical Stem Cells

 
Dr. Roy Eappen is a conservative, Christian, endocrinologist living in Montreal (Quebec, Canada). He writes a blog called Dr. Roy's Thoughts. The blog is richly decorated with all of the stereotypical symbols of the Blogging Tory that Canadian Cynic is so fond of (see example on left).

One of the thoughts Dr. Roy had recently concerns "Ethical" stem cells. This is a reference to recent work developing stem cell lines from somatic cells [see OK. Everyone take a deep breath ....].

Here's what Dr. Roy says,

This is an interesting article about Dr James A. Thomson. I have spoken to scientists on these matters before and all of them have been uneasy about using embryos for stem cells. They have said that they wanted to help the sick. While healing the sick is an admirable goal, one has to think of the moral cost as well.

Dr. Roy must hang out with a different class of scientists than the ones I see. Most of the scientists I know have few qualms about creating human stem cell lines from discarded human embryos.

This doesn't mean that there are no scientists in Canada who don't share Dr. Roy's opinions about abortion. It just means that Dr. Roy is very likely not telling the truth when he says that "all of them" are uneasy. Why is it that truthiness and Christianity don't often go together?

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[Hat Tip: Canadian Cynic ( Stem cells and reality. Because we're NOT morons.)]

Seymour Benzer (1921 - 2007)

Seymour Benzer died last Friday. In the 1950's and 1960's Benzer was a prominent member of the 'phage group founded by Max Delbrück and Salvador Luria [The Nobel Prize in Physiology or Medicine 1969.].

Benzer was best known for his detailed mapping of the rII locus in bacteriophage. Benzer was able to resolve mutants that were likely to be only a single nucleotide apart. His work on mapping deletions led directly to the conclusion that the genetic codon should consist of three nucleotides. In honor of Seymour Benzer, John Dennehy has selected his 1955 paper as this week's citation classic [Benzer, S. (1955)].

You can read about Benzer's famous experiments in the article he wrote for Phage and the Origins of Molecular Biology: Adventures in the rII region.

Later on in his career, Benzer worked with Drosophila melanogaster studying behavioral mutations, including some that affect the circadian rhythm. Since this is Coturnix's field, he has posted his own tribute to Benzer [In Memoriam: Seymour Benzer].

Other notable tributes:

Carl Zimmer [Farewell, Seymour Benzer].

PZ Myers [We've lost a great one: Seymour Benzer].

It's sad to note that most younger scientists, and almost all undergraduates, have never heard of Seymour Benzer. Mostly this is sad because it makes me realize how old I am!

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[Photo Credit: The photo shows Francis Crick (left) speaking to Seymour Benzer in 1964 (The Francis Crick Papers)]

Monday's Molecule #54

 
Name this molecule. Make sure you get the correct scientific name and the correct form of the molecule.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the Nobel Laureate(s) who worked out the function of the molecule.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: No winner this week. Several people got the correct molecule—it's the semiquinone form of flavin mononucleotide (FMN). One person guessed the Nobel Laureate but did not get the molecule correct.

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How Does an Intelligent Design Creationist Write a Ph.D. Thesis?

 
Some of you will remember Marcus Ross. He is a Young Earth Creationist who obtained a Ph.D. in paleontology from the University of Rhode Island [Lying for Jesus]. Ross now has a faculty position at Liberty University where he teaches courses in religion and science. PZ Myers has posted an update on his career [So what's Marcus Ross up to nowadays?].

How could Ross write an acceptable Ph.D. thesis if he believes that the Earth is less than 10,000 years old? We know the answer to this question. Ross did not discuss his true beliefs in his thesis or during his Ph.D. oral exam. Instead, he wrote a thesis on the fossil record as though he accepted the scientific age of the Earth. In other words, Ross said one thing in public lectures and another in the exam room.

I was reminded of this episode while listening to Kirk Durston last week in Denyse O'Leary's course. Kirk is a Ph.D. candidate in biophysics at the University of Guelph [Kirk Durston's Proof of God]. At some point he will write scientific papers and a thesis and he will be examined on his understanding of science. I wonder what he will do?

In his talk, Kirk tried very hard to give the impression that his scientific findings point to the existence of an intelligent designer. There was a brief mention of the distinction between science and philosophy but it wasn't at all clear whether he was stepping over the line or not. He concludes that God the intelligent designer exists.

One thing was clear, however. Kirk claimed that his work demonstrated the impossibility of evolving protein folds. He presented some calculations showing the total number of mutations that could have occurred since life began (10⁴¹, if I remember correctly). Then he showed that it would take far more than 10⁴¹ mutations to evolve the known protein folds.

In his lecture he clearly states that the results refute "Darwinism." He repeated over and over again that his thesis work was scientific evidence against evolution and in favor of intelligent design creationism.

It seems to me that Kirk Durston has only two choices at this point. Either he's sincere about his "scientific" claims, in which case they go into his thesis, or, alternatively, he's willing to disguise his true "scientific" conclusion by writing a thesis that's more likely to be accepted by the scientists on his committee.

To my way of thinking, scientific integrity should not be compromised in order to get a degree by trickery. But this presents a serious problem for Intelligent Design Creationists. In their public lectures, and in articles for the popular press, they make a big deal about the "scientific" nature of their findings. If that's what they truly believe then they should have no qualms about defending it in a scientific context. In other words, it goes in the thesis and let the chips fall where they may.

But here's the rub. Intelligent Design Creationists know full well that their version of science will not pass scrutiny by other scientists. Kirk Durston will not get his Ph.D. if he's being honest about his belief in his findings. It is simply not true that protein folding is scientific proof of intelligent design and a refutation of evolution.

So, Kirk like other creationists before him, will write the thesis that his committee will pass and not the one that he would be writing if he were honest.

The next hurdle will be the Ph.D. oral exam. Members of his committee know that he has been making very vocal claims about the significance of his Ph.D. research. They know that he has been making claims that the work refutes evolution even if that's not what's in the thesis. Should they question him about the difference between what he says in the thesis and what he says on the lecture circuit? Do they have a right to fail him if they think that what's in his thesis does not reflect his true opinion about the science—and that his true opinion is scientifically invalid?

I think the committee has this right and I think that a Ph.D. candidate should be prepared to defend any "scientific" claims they make outside of the lab.

There will be a few other problems with Kirk's thesis but they are easily fixed. For example, he claimed that ancient bacteria were complex and subsequent evolution has just been degradation of the genome. In the lecture he showed us several references. We now know that he is misinterpreting these scientific papers.

I assume this will go in the thesis because Kirk seemed to be really sincere when he talked about this as scientific fact. Member of his committee will read the thesis, correct his misconceptions, and point him to other scientific papers that reveal the true nature of bacterial evolution. This will give him an opportunity to learn about good science. At the end of the process Kirk will not be making scientifically inaccurate statements in public because he will know better.

There are quite a few examples of these factual errors but I assume they will all be fixed before the oral exam.

The bottom line is can Kirk Durston get a Ph.D.? If so, how should he do it? What do you think?

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[Photo Credit: Theses from Jackson State University]

What Is Evolution?

 
Greg Laden has just posted this video on his blog [Evolution ... Its for real]. I assume Greg endorses the definition of evolution in the opening minutes.

On Tuesday and Wednesday evenings I gave lectures on Evolution Is a Theory and a Fact. The first part of the lecture was devoted to explaining What Is Evolution. Here's the minimal scientific definition of evolution.

Evolution is a process that results in heritable changes in a population spread over many generations.

I explained to the audience that the definition of evolution has to be neutral with respect to mechanism. Evolution could occur by Lamarckian or Darwinian mechanisms, or something else entirely different.

The purpose of a definition is to define what we mean by the word. If we were to define evolution as that form of change caused by meiotic drive then change by natural selection wouldn't be evolution. How silly is that?

It's just as wrong to define evolution in terms of natural selection. That means random genetic drift is not evolution, by definition. Is that right?

The opening screen of the video states "The world is full of misinformation." The second screen says, "Many of those who claim evolution is wrong have no understanding what evolution really is."

This is exactly how I begin my talk. However, from that point on my lecture diverges considerably from the video that cdk007 created. Do you agree with the definition in the video? (Natural selection + time = EVOLUTION)

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Take a Short Quiz on Cheating - Do You Agree with the First Year Engineering Students?

 
What freshman engineering students think about cheating.

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More Misconceptions About Junk DNA

 
iayork of Mystery Rays from Outer Space is upset about an article on retroviruses that appeared in The New Yorker [ “Darwin’s Surprise” in the New Yorker]. Here's what iayork says,

The whole “junk DNA” has been thrashed out a dozen times (see Genomicron for a good start). The bottom line? If you search Pubmed for the phrase “junk DNA” you will find a total of 80 articles (compare to, say, 985 articles for “endogenous retrovirus”); and a large fraction of those 80 articles only use the phrase to explain what a poor term it is. Scientists don’t use the term “junk DNA’. Lazy journalists use it so they can sneer at scientists (who don’t use it) for using it.

Wrong! Lots of scientists use the term "junk DNA." Properly, understood, it's a very useful term and has been for several decades [Noncoding DNA and Junk DNA].

Yes, it's true that journalists often don't understand junk DNA and they are easily tricked into thinking that junk DNA is a discredited concept. The journalists are wrong, not the scientists who use the term.

It's also true that there are many scientists who feel uneasy about junk DNA because it doesn't fit with their adaptationist leanings. Just because there's controversy doesn't mean that the term isn't still used by it's proponents (I am one).

I'm sorry, iayork, but statements like that don't help in educating people about science. Junk DNA is that fraction of a genome that has no known function and based on everything we know about biology is unlikely to have some unknown function. Junk DNA happens to represent more than 90% of our genome and that's significant by my standards.

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Agassiz in the Concrete and Persecution of Religious Scientists

John Pieret has a posting on possible examples of persecution of religious scientists in the nineteenth century [On the Ways of Change].

John quotes from a book by Neal C. Gillespie on Charles Darwin and the Problem of Creation. Gillespie is discussing the conflict between religion and science among academics in the mid-1800's. According to John, Gillespie says,

Antagonism against biblicism had reached such a point by the late 1850s that Agassiz suggested that fear of the wrath of the positivists was actually leading some naturalists with strong theological convictions to conform to the new science against their true judgment.

The quote refers to Louis Agassiz, a biology Professor at Harvard^1. and one of the last holdouts against evolution. John links to the upcoming Expelled movie and asks whether Agassiz is referring to persecution of religious scientists.

John posted a photograph of the statue of Louis Agassiz embedded upside down in the courtyard in front of the zoology building at Stanford University. The statue tumbled from its place above the entrance during the San Francisco earthquake of 1906.

According to legend, a passing scientist remarked that,

Louis Agassiz was better in the abstract than in the concrete.^2.

This is a clear reference to the fact that Agassiz's reputation had been severely damaged by his religious convictions and his rejection of biological evolution.

Is it true that atheist scientists discriminate against religious scientists? John has been concerned about this issue for a number of years. He thinks that atheist scientists fail to distinguish between real science and metaphysics. He thinks that much of our criticism of religious scientists is not because we're scientists but because we're atheists.

I'm posting a specific case for consideration in another message so it was quite appropriate, and fortuitous, that John Pieret brought it up today on Thoughts in a Haystack.

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1. Stephen Jay Gould held the Alexander Agassiz Professor of Zoology Chair at Harvard from 1982 until his death in 2002. Alexander Agassiz was Louis Agassiz's son. Alexander served as President of the National Academy of Sciences.

2. The story is apocryphal (a polite word for "false"). The quotation has been attributed to several men, including the President of Stanford, but all have denied it. Nevertheless, it's too good a story to abandon just because it happens to be untrue!

[Photo Credit: Wikipedia]

Evolution and Purpose

 
The first issue of Evolution: Education and Outreach is available online [Contents]. You can read all 21 articles.

Many of them are very interesting but I'm particulary struck by one with the title The Question of Purpose by David Zeigler. The question of purpose in evolution is very contentious. If we stick to science, it's clear that there is no purpose to evolution. What this means is that science is at odds with every religious belief that requires purpose (e.g., God made us).

Many believers resist this interpretation of science by declaring that conclusions about the absence of purpose cross over into the realm of metaphysics. Therefore, science does not rule out a purposeful universe.

David Zeigler is having none of that kind of excuse ...

My “purpose” (we can create our own temporally and spatially limited purposes) in writing this piece is to point out one of the most important and real issues in the teaching of Darwinian evolution that so often goes unaddressed, or more amazingly—unrecognized, and this issue is really fairly obvious. Darwinian evolution by natural selection results in adaptations which increase the ability of the individuals to survive and reproduce successfully in their respective environments, or as biologists would say—adaptations increase the fitness of individuals. This is the only evolutionary goal or purpose for which science has found objective evidence.

In our science, there is no mention of, or mechanism for achieving, any long-term metaphysical or teological goals of form, complexity, or intelligence—as Gould has argued so eloquently. Most of the other known mechanisms of evolutionary change such as genetic drift, neutral mutation, gene duplications, transposons, horizontal gene transfer by plasmids, and others have no direction or goal at all and are in fact random (which natural selection is not) and therefore could not possibly give a particular direction to evolution. Numerous science writers have made the obvious point that had that asteroid not struck some 65,000,000 years ago and pushed the dinosaurs to extinction, we humans would undoubtedly not be here, for the evolution of mammals would have been constrained and altered drastically from what has come to pass (i.e., we humans were not destined to evolve).

If we teach evolution honestly, we cannot really avoid this point, although many succeed in doing so. Additionally, if we give any credence to some hybrid form of teleological evolution by which humans or any of the so-called “higher” forms were destined to appear, we have gutted Darwinian evolution of its scientific core and replaced it with an unfounded belief—one that too many of our students (and most intelligent design proponents) already hold. I believe it is in part because we tiptoe around the honest interpretation of Darwinism that the USA lags far behind the other developed countries of the world in accepting the modern scientific view of evolution and in taking a realistic view of our precarious place (and responsibilities) on this fragile planet.

I don't like his use of "Darwinism" as an incorrect substitute for "biological evolution" but it's otherwise a fine piece. If this is an indication of the quality of article that will appear in the new journal then I'll be looking forward to each issue.

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Evolution as Fact, Theory, etc.

 
Ryan Gregory has just published an essay in Evolution: Education and Outreach on Evolution as Fact, Theory, and Path [see Genomicron].

Ryan has made of list of similar essays on the web. I reproduce that list here except I'm linking to the latest version of my essay (2007) rather than the 1993 version that's on the TalkOrigins.org website.

• Evolution as fact, theory, and path (T. Ryan Gregory)


• Evolution: fact and theory (Richard E. Lenski)


• The fact of evolution: implications for science education (James R. Hofman and Bruce H. Weber)
  


• Evolution is a fact and a theory (Larry Moran)
  


• Evolution as fact and theory (Stephen Jay Gould)
  

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Why We Call them IDiots

 

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[Hat Tip: Monado at Science Notes ( Why do people laugh at Creationists? 4)]

Nobel Laureates: Edmond Fischer and Edwin Krebs

 

The Nobel Prize in Physiology or Medicine 1992.

"for their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism"

Edmond H. Fischer (1920 - ) and Edwin G. Krebs (1918 - ) received the Nobel Prize in Physiology or Medicine for working out the pathway for regulation of glycogen metabolism. The main feature of this regulation is the phosphorylation and dephosphorylation of enzymes to control their activity [Regulating Enzyme Activity by Covalent Modification].

The Nobel Lectures by Ed Krebs [Protein Phosphorylation and Cellular Regulation I] and Ed Fischer [Protein Phosphorylation and Cellular Regulation II] should be required reading for all biochemistry students. Not only do they show how a fruitful collaboration works, they provide an excellent introduction to fundamental aspects of metabolism and regulation. I wouldn't be surprised if some of the material in these lectures appeared on introductory biochemistry exams.

For this Nobel Prize there's a slide presentation on the Nobel Prize website illustrating the work done by Ed Fischer and Ed Krebs [Illustrated Presentation]. Fischer and Krebs are Professors Emeritii at the University of Washington (USA). They have been friends and collaborators for many years. The first illustration (below) is from the slide presentation.

The Nobel Prize website also has video links to interviews with Edmond Fischer and the transcript of an interview with Edmond Krebs. Here's an excerpt from the interview with Krebs ...

Edwin G. Krebs is a soft-spoken, understated Midwesterner, but there's one thing that gets his goat. Since he turned his attention from medicine to biochemistry, people have been asking him about "his" cycle. They confuse him with Sir H.A. Krebs, the British scientist who won the Nobel Prize in 1953 for elucidating the metabolic Krebs (or tricarboxylic acid) cycle.

One person who made this mistake was the chairman of a clinical department at the UW School of Medicine in 1948, when Krebs started as an assistant professor of biochemistry.

"I must confess that I didn't correct his wrong impression," says Krebs. "I was so uneasy about my status then that I enjoyed being treated with such deference, even for the wrong reason."

The Nobel Prize presentation speech was delivered by Professor Hans Jörnvall of the Nobel Assembly of the Karolinska Institute.

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

This year's Nobel Prize in Physiology or Medicine is awarded for discoveries concerning reversible protein phosphorylation. What does that mean and how does phosphorylation work?

Let us start with proteins. They can be compared with workers in our tissues. We are composed of cells, each cell constituting a small community. Constant activity is a characteristic feature both of cells and ordinary communities. There are systems for transportation, energy generation, production, and waste handling. In society all this is handled by humans, in a cell proteins take our place. How do they accomplish their functions? Well, exactly like human workers, they operate by way of interaction with other components. Much in the same manner as a driver or pilot recognizes the controls, proteins recognize "their" partners, binding them to influence the reaction paths.

And now phosphorylation: one or several small phosphate groups are coupled to a protein, changing its properties. If the parallel with our human workers is pursued further, one could perhaps compare phosphorylation with ballet shoes. Despite their small size they have dramatic effects on their wearer! The shape of the foot is altered and after that, work is like a dance. Edmond Fischer and Edwin Krebs, this year's Laureates, described this principle in the ftfties. They showed how muscles liberate an energy-rich form of sugar from its storage form by phosphorylation of a protein. After that, science gradually gained insight into the fact that this constitutes a general principle manifested in all cellular activities. Today, a considerable part of world bioscience involves protein phosphorylation.

THEME:

Nobel Laureates
Why this regulation via coupling of small groups? One advantage is that the process is reversible, i.e. the shoes can be taken off and put on, a process which can be repeated again and again. Thus, proteins can be regulated in both directions. Another is that the reactions can be carried out in successive steps, creating a cascade that amplifies the end effect. Much like the hydraulic amplification in a brake: a gentle touch of the pedal can stop even a heavy car. In the world of proteins, Krebs and his collaborators paved the way for this knowledge by studying also the preceding protein in the chain of phosphorylations, while Fischer concentrated his efforts along other lines and, as recently as some years ago, reported the purification of a special type of phosphate-removing protein.

Yet another advantage is that the regulation can be affected by different signals. The system that Fischer and Krebs first studied can be activated either by means of a stress hormone released when we become frightened and our muscles prepare us for escape, or by an act of will when we wish to run for other reasons. Phosphate groups are in these two cases attached in response to separate signals, much as they are in all other cellular response systems. What relevance does this have to medicine? The easiest answer is that we all know of the consequences in society from imbalances in economic chain reactions! We are now in a position to start perceiving how illnesses, including common diseases like hypertension and tumors, are accompanied by imbalances in phosphorylations. Relationships initially recognized in connection with glycogen storage in muscles and liver, have thus been proven to pertain to cellular regulatory processes in general. An excellent demonstration of the power of basic research and of the versatility of simple models. The protein system in glycogen storage has given rise, over the years, to several Nobel Prizes, in 1947 to Gerty and Carl Cori for the course of the catalytic conversion of glycogen, in 1971 to Earl Sutherland for mechanisms of action of hormones, and now to Fischer and Krebs for discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism.

Edmond Fischer and Edwin Krebs,

I have tried to describe your field of research and elegant discoveries in your studies of reversible protein phosphorylation, going back to the initial detection of the activation mechanism of phosphorylase, and continuing with protein phosphatases. Over the years, your early observations on a particular system have contributed to the opening up of novel insight into basic protein regulations at all levels and in all cells. On behalf of the Nobel Assembly of the Karolinska Institute, I convey to you our warmest congratulations, and ask you now to step forward to receive your Nobel Prizes from the hands of His Majesty the King.

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[Photo Credit: Dept. of Biochemistry, University of Washington]

Regulating Enzyme Activity by Covalent Modification

 
Monday's Molecule #53 was phosphothreonine, one of several amino acid residues that can be phosphorylated.

UPDATE= The other major ones are serine and tyrosine but histidine, lysine, cysteine, aspartate and glutamate can also be phospohylated in some proteins as well as some modified amino acids like hydroxy-proline (Reinders, and Sickmann 2005).


Enzyme activity can be modified by covalent attachment of a phosphoryl group to an amino acid residue. In some cases the phosphorylated enzyme will be active while in other cases the phosphorylated enzyme will be inactive.

The classic examples of regulation by covalent modification are in the pathways for synthesis and degradation of glycogen [Regulating Glycogen Metabolism]. For example, the enzyme glycogen phosphorylase is responsible for breaking down glycogen and liberating glucose. Glycogen phosphorylase is active when phosphorylated and inactive when the phosphoryl group is removed. The phosphorylation is carried out by phosphorylase kinase and this enzyme is, itself, regulated by covalent modification. These enzymes are part of a larger signal transduction pathway involving several different phosphorylated enzymes.

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Reinders, J. and Sickmann, A. (2005) State-of-the-art in phosphoproteomics. Proteomics 5:4052-4061.

Evolution Is a Theory and a Fact

 
Don't forget about my talk tonight at McMaster University in Hamilton (Ontario, Canada). It's sponsored by the McMaster Association of Secular Humanists (MASH) (Hamilton) [Evolution is a Theory and a Fact, with Prof Laurence Moran]

The subject is Evolution Is a Theory and a Fact. Come to room HSC/1A1 at 7pm. (HSC is the (Health Sciences Building, or the Hospital, map here.)

Cost: $2 (free for members of the MASH)

Tomorrow night I'm at the Centre for Inquiry, 216 Beverley Street in Toronto. (Beverly St. is the southward extension of St. George St. The Centre is on the west side of the street about one block south of College.)

The talk begins at 7pm.
Cost: $4 (*special announcement: students Free*) FREE for Friends of the Centre

The public event at CFI will also serve as the official launch of Cafe Inquiry, a project of the University of Toronto Secular Alliance, sponsored by CFI Ontario. Similar to Cafe Scientifique hosted by the Ontario Science Centre, we will serve food and beverages and encourage discussion with the audience. Bring your questions and comments on this controversial issue!

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I'm Looking Through You

 
John Wilkins of Evolving Thoughts has posted a goodbye tribute to John Howard [Beatles' ode to John Howard]. Like all bloggers over 40—or maybe 50—whenever you read the lyrics to "I'm Looking Through You" you can't help but sing along, can you?

For all you youngsters out there, here's how to sing the song ....

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